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• Anti-TIGIT antibody tiragolumab improves PD-L1 blockade via myeloid and Treg cells

  Tiragolumab, an anti-TIGIT antibody with an active IgG1/kappa Fc, demonstrated improved outcomes in the phase 2 CITYSCAPE trial (NCT03563716) when combined with atezolizumab (anti-PD-L1) versus atezolizumab alone1. However, there remains little consensus on the mechanism(s) of response with this combination2. We found that high baseline intratumoral macrophages and Tregs were associated with better outcomes in patients treated with atezolizumab plus tiragolumab but not with atezolizumab alone. Serum sample analysis revealed that macrophage activation was associated with clinical benefit in patients receiving the combination treatment. In mouse tumor models, tiragolumab surrogate antibodies inflamed tumor-associated macrophages, monocytes, and dendritic cells through Fc gamma receptors (FcɣR), in turn driving anti-tumor CD8+ T cells from an exhausted effector-like state to a more memory-like one. These results uncover a mechanism of action by which TIGIT checkpoint inhibitors can remodel immunosuppressive tumor microenvironments, and suggest that FcɣR engagement is an important consideration in anti-TIGIT antibody development.

  Study EGAS50000000251

• Botensilimab, an Fc-enhanced Anti-CTLA-4 Antibody, is Effective Against Tumors Poorly Responsive to Conventional Immunotherapy

  This study explores the genomic landscape associated with a novel Fc-engineered anti-CTLA-4 antibody (botensilimab) in advanced solid tumors. We seek to understand if enhancing the Fc-region affinity of anti-CTLA-4 antibodies can improve anti-tumor efficacy and expand clinical benefit to tumors poorly responsive to conventional immunotherapy. As part of an ongoing open-label, Phase 1, multicenter study, we conducted an exploratory sub-analysis of genomics data. The primary study evaluates the safety, tolerability, pharmacokinetics, and pharmacodynamics of botensilimab monotherapy and in combination with an anti-PD-1 antibody (balstilimab) in participants with advanced solid tumors. RNA from formalin-fixed paraffin-embedded (FFPE) tumor biopsies and matched normal blood samples were isolated and subjected to RNA-sequencing using the Personalis ImmunoID NeXT Platform. We demonstrated that anti-CTLA-4 engineered for enhanced FcγR affinity leverages FcγR-dependent mechanisms to potentiate T cell responsiveness, reduce intratumoral Tregs, and enhance antigen presenting cell activation. This genomic analysis contributes to our understanding of the molecular mechanisms underlying patient responses to Fc-engineered anti-CTLA-4 therapy and may inform future strategies to expand the clinical benefit of immune checkpoint blockade in cancer immunotherapy.

  Study phs003704

• Characterization of a human iPSC-derived endocrine pancreas model

  Directed differentiation of stem cells offers a scalable solution to the need for human cell models recapitulating islet biology and T2D pathogenesis. We profiled mRNA expression at six stages of an induced pluripotent stem cell (iPSC) model of endocrine pancreas development from two donors, and characterized the distinct transcriptomic profiles associated with each stage. Established regulators of endodermal lineage commitment, such as SOX17 (log2 fold change [FC] compared to iPSCs=14.2, p-value=4.9x10-5) and the pancreatic agenesis gene GATA6 (log2 FC=12.1, p-value=8.6x10-5), showed transcriptional variation consistent with their known developmental roles. However, these analyses highlighted many other genes with stage-specific expression patterns, some of which may be novel drivers or markers of islet development. For example, the leptin receptor gene, LEPR, was most highly expressed in published data from in vivo-matured cells compared to our endocrine pancreas-like cells (log2 FC=5.5, p-value=2.0x10-12), suggesting a role for the leptin pathway in the maturation process. Endocrine pancreas-like cells showed significant stage-selective expression of adult islet genes, including INS, ABCC8, and GLP1R, and enrichment of relevant GO-terms (e.g. "insulin secretion"; odds ratio=4.2, p-value=1.9x10-3): however, principal component analysis indicated that in vitro-differentiated cells were more immature than adult islets. Integration of the stage-specific expression information with genetic data from T2D genome-wide association studies revealed that 46 of 82 T2D-associated loci harbor genes present in at least one developmental stage, facilitating refinement of potential effector transcripts. Together, these data show that expression profiling in an iPSC islet development model can further understanding of islet biology and T2D pathogenesis.

  Study EGAS00001001803

• Fgl2 Regulates FcγRIIB+ CD8+ T Cell Responses during Infection

  While the inhibitory receptor FcγRIIB has been shown to be upregulated on activated CD8+ T cells in both mice and humans, its impact on T cell fate during infection has not been fully elucidated. We identified an increase in FcγRIIB-expressing CD8+ T cells in COVID patients relative to healthy controls, and in mouse models of viral infection. Despite its well-known role as an Fc receptor, FcγRIIB also ligates the immunosuppressive cytokine Fgl2, resulting in CD8+ T cell apoptosis. Both chronic LCMV infection in mice and COVID in humans resulted in a significant increase in plasma Fgl2. Further, plasma Fgl2 was directly proportional to CD8+ T cell lymphopenia in COVID patients. To further understand the association of Fgl2 and CD8+ T cell lymphopenia following COVID infection, we assessed the transcriptomic profiles of PBMCs with high (≥ 9.153 ng/ml) vs low (defined as

  Study phs003870

• Expression profiling of a human endocrine pancreas iPSC model

  Directed differentiation of stem cells offers a scalable solution to the need for human cell models recapitulating islet biology and T2D pathogenesis. We profiled mRNA expression at six stages of an induced pluripotent stem cell (iPSC) model of endocrine pancreas development from two donors, and characterized the distinct transcriptomic profiles associated with each stage. Established regulators of endodermal lineage commitment, such as SOX17 (log2 fold change [FC] compared to iPSCs=14.2, p-value=4.9x10-5) and the pancreatic agenesis gene GATA6 (log2 FC=12.1, p-value=8.6x10-5), showed transcriptional variation consistent with their known developmental roles. However, these analyses highlighted many other genes with stage-specific expression patterns, some of which may be novel drivers or markers of islet development. For example, the leptin receptor gene, LEPR, was most highly expressed in published data from in vivo-matured cells compared to the endocrine pancreas-like cells (log2 FC=5.5, p-value=2.0x10-12), suggesting a role for the leptin pathway in the maturation process. Endocrine pancreas-like cells showed significant stage-selective expression of adult islet genes, including INS, ABCC8, and GLP1R, and enrichment of relevant GO-terms (e.g. “insulin secretion”; odds ratio=4.2, p-value=1.9x10-3): however, principal component analysis indicated that in vitro-differentiated cells were more immature than adult islets. Integration of the stage-specific expression information with genetic data from T2D genome-wide association studies revealed that 46 of 82 T2D-associated loci harbor genes present in at least one developmental stage, facilitating refinement of potential effector transcripts. Together, these data show that expression profiling in an iPSC islet development model can further understanding of islet biology and T2D pathogenesis.

  Dataset EGAD00001002148

• Transcriptomic Characterization of Human Innate T Cells

  We performed low input RNA-seq and single-cell RNA-seq on 7 lymphocyte populations with the objective of finding the common transcriptional programs shared among innate T cells. In brief, we drew blood from healthy donors and isolated CD4+ T cells, CD8+ T cells, Natural Killer cells, invariant natural killer T (iNKT) cells, mucosal-associated invariant T (MAIT) cells, and two γδ T cell populations: Vδ1 and Vδ2. We performed low input RNA-seq on samples with 1000 cells each, for 6 healthy individuals, in duplicate. We performed single-cell RNA-seq with DNA-barcoded hashing antibodies to identify the cell type of origin for each cell. We found a common transcriptional program across lymphocytes that is gradually turned on as lymphocytes have a more "innateness" state, promoting effector functions and sacrificing proliferative capacity. Additionally, we performed low input RNA-seq for Vδ3-expressing γδ T cells and δ/αβ T cells for one healthy individual in duplicate (1000 cells per sample). This revealed δ/αβ T cells are transcriptionally more adaptive-like and Vδ3 more innate-like.

  Study phs002007

• A Dose Escalation Study of Efmarodocokin Alfa (UTTR1147A) in Healthy Volunteers and Patients with Ulcerative Colitis

  Background: The interleukin-22 cytokine (IL-22) has demonstrated efficacy in nonclinical colitis models with a non-immunosuppressive mechanism-of-action. Efmarodocokin alfa (UTTR1147A) is a fusion protein agonist that links IL-22 to the crystallizable fragment (Fc) of human immunoglobulin (IgG4) for improved pharmacokinetic characteristics, but with a mutation to minimize Fc effector functions. Methods: This randomized, phase 1b study evaluated the safety, tolerability, pharmacokinetics, and pharmacodynamics of repeat intravenous dosing of efmarodocokin alfa in healthy volunteers (HVs; n=32) and patients with ulcerative colitis (UC; n=24) at 30–90 µg/kg doses given biweekly (Q2W) or monthly (Q4W) (6:2 active:placebo per cohort). Results: The most common adverse events (AEs) were on-target dermatological effects (dry skin, erythema, and pruritus) that were reversible. Dose-limiting non-serious dermatological AEs (severe dry skin, erythema, exfoliation, and discomfort) were seen in two HVs and one patient at 90 ug/kg Q2W. Pharmacokinetics were generally dose-proportional across the dose levels tested, but patients demonstrated lower drug exposures relative to HVs at the same dose. IL-22 serum biomarkers and IL-22 responsive genes in colon biopsies were induced with active treatment. Patients demonstrated changes in microbiota composition following active treatment, thereby reversing baseline dysbiosis. Clinical response was observed in 7/18 active- and 1/6 placebo-treated patients; clinical remission was observed in 5/18 active- and 0/6 placebo-treated patients.

  Study EGAS00001006172

• Data Access Committee KCL FC

  Dac EGAC00001000386

• Disease specific alterations in the olfactory mucosa of patients with Alzheimer’s disease

  The sample AD_Library_1, AD_Library_2 and Control_Library were run on a Chromium Chip B with the Chromium Single Cell 3′ Library & Gel Bead Kit v3 kit (10x Genomics, CA, USA) . The 3’ gene expression libraries were sequenced at an approximate depth of 50,000 reads per cell using the NovaSeq 6000 S1 (Illumina, San Diego, CA, USA) flow cells. Cell Ranger v.3.0.2 was used to analyze the raw base call files. FASTQ files and raw gene-barcode matrices were generated and aligned human genome GRCh37 (hg19). The samples were integrated in R v.4.0.3 and generated Seurat objects, two related to AD samples and one to control samples, were analyzed using the Seurat package v.4.0.3 to perform downstream analysis, clustering of the cells and differential expression.

  Dataset EGAD00001008560

• SG Peranakan Project dataset

  This dataset contains the genotypes jointly-called from whole genome sequencing data of 177 self-reported Peranakans in Singapore. Reads were aligned to GRCh37 reference genome and jointly-called with other WGS samples. Basic quality control measures and population phasing without reference were performed on the called genotypes. The data are stored in VCF v 4.3 format, and one .vcf.gz file stored the genotypes from one of the 23 chromosomes (22 autosomes+X chromosome).

  Dataset EGAD00001007786

• MCF10A 12h IL6 classical signaling

  Gene expression after cell culture, 12h IL6+sgp130-Fc stimulated

  Dataset EGAD00010001970

• MCF10A 24h IL6 classical signaling

  Gene expression after cell culture, 24h IL6+sgp130-Fc stimulated

  Dataset EGAD00010001963

• H3.3G34R/V-transformed interneuron progenitors co-opt PDGFRA for gliomagenesis

  Histone H3.3 glycine 34 to arginine/valine (H3.3G34R/V) mutations occur in deadly hemispheric high-grade gliomas. These tumors show exquisite regional and temporal specificity, suggesting a developmental context permissive to the effects of G34R/V mutations. Here we present the molecular landscape of G34R/V gliomas (n=85) and show that 50% bear activating mutations in PDGFRA, with strong selection pressure for PDGFRAMUT clones at recurrence. We show that G34R/V tumors arise in interneuron progenitors of the foetal ventral forebrain expressing GSX2 and the DLX family of homeobox transcription factors, where terminal neuronal differentiation is impaired through aberrant G34R/V-mediated H3K27me3. Frequent co-occurrence of G34R/V & PDGFRAMUT is facilitated in this interneuron lineage-of-origin as PDGFRA forms an aberrant chromatin loop with the adjacent GSX2, hijacking its active chromatin conformation. At the single-cell level, G34R/V tumours entirely lack oligodendroglial transcriptional programs prominent in other glioma entities, and instead harbour dual neuronal and astroglial compartments. CRISPR-removal of H3.3G34R/V does not impact tumorigenicity suggesting this mutation becomes dispensable, while PDGFRAMUT are potently oncogenic regardless of G34 mutation. Collectively, our results suggest that G34R/V gliomas arise in foetal interneuron progenitors unable to undergo terminal differentiation, enabling co-option of PDGFRA through inappropriate expression and activating mutations to promote gliogenesis and oncogenicity. Reliance on PDGFRA for oncogenesis may be of therapeutic opportunity in G34R/V glioma.

  Study EGAS00001004301

• Spatial whole exome sequencing of metastatic melanoma

  We performed whole exome sequencing of 8 samples derived from a patient with metastatic melanoma. These represent six different regions of a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor, one pre-treatment biopsy that was treatment naive and one post-PD-1 inhibitor treated lesion. Exome sequencing data was generated using methods as previously described, including library preparation using the Agilent SureSelect XT Target Enrichment protocol (#5190-8646) prior to sequencing on an Illumina HiSeq 2000/2500 v3 system using 76bp paired-end reads. Raw sequencing data was then processed using Saturn V, the next generation sequencing data processing and analysis pipeline developed by the Department of Genomic Medicine at the UT MD Anderson Cancer Center.

  Dataset EGAD00001005819

• Excised DNA Circles from V(D)J Recombination Promote Relapsed Leukaemia

  In this study, we show that ESCs replicate and persist through many cell generations. High ESC copies at diagnosis of BCP-ALL strongly correlate with subsequent relapse. These data provide the first demonstration that the V(D)J recombination by-product, when replicated to elevated levels, potently associates with the V(D)J recombinase to cause adverse disease outcomes.

  Study EGAS50000001043

• Excised DNA Circles from V(D)J Recombination Promote Relapsed Leukaemia

  In this study, we show that ESCs replicate and persist through many cell generations. High ESC copies at diagnosis of BCP-ALL strongly correlate with subsequent relapse. These data provide the first demonstration that the V(D)J recombination by-product, when replicated to elevated levels, potently associates with the V(D)J recombinase to cause adverse disease outcomes.

  Study EGAS50000000407

• Ribo-depleted RNA-sequencing of II.3, III.1, and III.3

  This datasets contains the Ribo-depleted RNA-sequencing of patients II.3, III.1, and III.3. Libraries were sequenced to a minimum depth of 195 million read pairs (2x75nts) on an Illumina NextSeq500 Midoutput FC.

  Dataset EGAD50000002364

• ISCAPE V(D)J libraries from HA-specific single memory B cells and personalized IGM, IGK, IGL V(D)J repertoire sequencing of four Influenza A exposed individuals

  Peripheral blood mononuclear cells were used to produce paired, full-length IGM, IGK and IGL V(D)J libraries from HA-binding single memory B cells using the ISCAPE (Individualized Single Cell Analysis of Paired Expressed antigen receptors) technique. Locus-specific multiplexed nested PCR with 5’ leader IGHV/IGKV/IGLV and 3’ constant IGG/IGK/IGL primer mixtures was performed before well and plate indexing and paired chain sequencing with an Illumina MiSeq instrument. Expressed total IGM, IGK and IGL V(D)J libraries from each donor were generated to define personalized IG allele content.

  Study EGAS50000001390

• Personalized IGM, IGK, IGL V(D)J repertoire sequencing of four Influenza A exposed individuals

  Peripheral blood mononuclear cells were used to produce paired, full-length IGM, IGK and IGL V(D)J libraries from HA-binding single memory B cells using the ISCAPE (Individualized Single Cell Analysis of Paired Expressed antigen receptors) technique. Locus-specific multiplexed nested PCR with primer sets targeting the 5’ UTR/leader and 3’ constant region was performed before well and plate indexing and paired chain sequencing with an Illumina MiSeq instrument. Expressed total IGM, IGK and IGL V(D)J libraries from each donor were acquired and analyzed to define personalized IG allele content. The fastq file names include the donor and target for expressed IGM, IGK or IGL V(D)J libraries.

  Dataset EGAD50000002018

• IgM heavy chain V(D)J library sequencing using varied PCR parameters

  When amplifying the rearranged V(D)J genes encoding antigen receptors during adaptive immune receptor repertoire sequencing (AIRR-seq), each cycle of the PCR can produce spurious “chimeric” hybrids of two or more different template sequences. To test the effects of PCR protocol variation on chimera formation in AIRR-seq, we produced IgM heavy chain V(D)J repertoire libraries under 8 conditions, varying the number of PCR cycles, indexing PCR template, input RNA, and extension time. Three donors were sequenced using all 8 conditions.

  Study EGAS50000001037

• Whole exome sequencing of endometriod ovarian cancer tumours

  Whole Exome sequencing data of tumour samples for 112 patients with endometrioid ovarian carcinoma in FASTQ format. Data was derived as summarized below: Library Preparation: Libraries were prepared from each DNA sample using the Illumina TruSeq Exome Library Prep kit (#FC-150-1002) according to the provided protocol using modifications for working with FFPE sourced material. Libraries were quantified using the Qubit 2.0 Fluorometer and the Qubit DNA HS assay (#Q32854) and the size distribution of fragments was assessed using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Library QC: Exome-captured sequencing library pools were quantified using the Qubit 2.0 Fluorometer and the Qubit DNA HS assay (#Q32854) and the size distribution of fragments was assessed using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Fragment size and quantity measurements were used to calculate molarity for each library pool. Sequencing: Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (# FC-404-2002) on the NextSeq 550 platform (Illumina Inc, #SY-415-1002).

  Dataset EGAD00001006389

• ISCAPE V(D)J libraries from HA-specific single memory B cells of four Influenza A exposed individuals

  Peripheral blood mononuclear cells were used to produce paired, full-length IGM, IGK and IGL V(D)J libraries from HA-binding single memory B cells using the ISCAPE (Individualized Single Cell Analysis of Paired Expressed antigen receptors) technique. Locus-specific multiplexed nested PCR with primer sets targeting the 5’ UTR/leader and 3’ constant region was performed before well and plate indexing and paired chain sequencing with an Illumina MiSeq instrument. Expressed total IGM, IGK and IGL V(D)J libraries from each donor were acquired and analyzed to define personalized IG allele content. The fastq file names include the donor and a numerical plate index for the HA-specific ISCAPE BCR HC and LC V(D)J libraries.

  Dataset EGAD50000002019

• RRBS of 25 pleural mesothelioma samples (Single-end)

  The dataset contains RRBS data (bam files) for 25 pleural mesothelioma samples.The samples were sequenced on NovaSeq6000 (Illumina, San Diego, CA) in single-end 150bp mode. RRBS raw reads were trimmed for adaptor sequences using trim galore (v. 0.6.5) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and filtered for low-quality sequences using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High quality trimmed reads were mapped to the Human reference genome (UCSC genome assembly GRCh38/hg38) using Bismark (v. 0.22.3) with default parameters.

  Dataset EGAD50000002130

• RRBS of 58 pleural mesothelioma samples (Paired-end)

  The dataset contains RRBS data (bam files) for 58 pleural mesothelioma samples. The samples were sequenced on NovaSeq6000 (Illumina, San Diego, CA) in paired-end 150bp mode. RRBS raw reads were trimmed for adaptor sequences using trim galore (v. 0.6.5) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and filtered for low-quality sequences using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High quality trimmed reads were mapped to the Human reference genome (UCSC genome assembly GRCh38/hg38) using Bismark (v. 0.22.3) with default parameters.

  Dataset EGAD50000002129

• Characterizing the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft model for RNA-based liquid biopsy in a preclinical setting

  This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n=171) derived from a DLBCL PDTX model including 27 humanized (HIS) PDTX, 8 HIS non-PDTX and 21 non-HIS PDTX NOD-scid IL2Rgnull mice were collected during humanization, xenografting, treatment, and sacrifice. The mice were treated with either R-CHOP, huCD20-Fc-AFN-CHOP, or phosphate-buffered saline (PBS). RNA was extracted using the miRNeasy serum/plasma kit and sequenced on the NovaSeq 6000 platform using the SMARTer Stranded Total RNA-seq pico v3 kit.

  Study EGAS50000000566

• High titers and low fucosylation of early phase anti-SARS-CoV-2 IgG promote hyper-inflammation by alveolar macrophages

  We show that early phase anti-Spike IgG in serum of critically ill COVID-19 patients induces hyper-inflammatory responses by human alveolar macrophages. We identified that this excessive inflammatory response is dependent on two antibody features that are specific for severe COVID-19. First, inflammation is driven by high titers of anti-Spike IgG, a hallmark of severe disease. Second, we found that anti-Spike IgG from severely ill patients is intrinsically more pro-inflammatory because of different glycosylation of the Fc tail, particularly by low fucosylation. This dataset is linked with the following ArrayExpress Experiment: E-MTAB-10431 - 2020_COVID19_FCGR_MIL10_IgGfucosylation

  Study EGAS00001005206

• Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma

  Follicular lymphoma (FL) is an incurable B-cell malignancy characterized by the t(14;18) and mutations in one or more components of the epigenome. Whilst frequent gene mutations in signaling pathways, including JAK-STAT, NOTCH and NF-κB, have also been defined, the spectrum of these mutations typically overlap with the closely-related diffuse large B cell lymphoma (DLBCL). A combination of discovery exome and extended targeted sequencing revealed recurrent somatic mutations in RRAGC uniquely enriched in FL patients (17%). More than half of the mutations preferentially co-occurred with ATP6V1B2 and ATP6AP1 mutations, components of the vacuolar H+-adenosine triphosphate ATPase (v-ATPase) known to be necessary for amino acid-dependent mTORC1 activation. RagC mutants increased raptor binding whilst rendering mTORC1 signaling resistant to amino acid deprivation through nucleotide-independent mechanisms. Collectively, the activating nature of the RRAGC mutations, their existence within the dominant clone and stability during disease progression supports their potential as an excellent candidate to be therapeutically exploited.

  Study EGAS00001001190

• Variables of diversity, clonality, V and J usage and main COVID-19-reactive GLIPH2 frequencies.

  Main results of the T cell repertorie analysis of a cohort of 61 patients. For each patient, repertorie diversity and clonality metrics, V an J alelle frequency and COVID-19-reactive sequencies have been calculated using open.source code. For more information about the study, please visit DOI: 10.1186/s40246-024-00654-0

  Study EGAS50000000587

• Identifying genetic variants that alter TCR usage in the peripheral repertoire

  The relationship between genetic variation and CD8+ T-cell receptor (TCR) repertoire usage in patients receiving Immune Checkpoint Blockade (ICB) therapy for cancer is unexplored. We have conducted a genome-wide and human leukocyte antigen (HLA)-focused analysis of CD8+ T-cell TCR repertoire to identify genetic determinants of variable gene (V-gene) and CDR3 K-mer usage from samples taken prior to and after ICB (n=250). We identify 11 cis and 10 trans V-gene associations, primarily to the MHC, that meet genome-wide significance. TCR clones containing HLA associated V-genes were less stable across treatment, whilst at the single-cell level, genetically associated clones demonstrate subset enrichment and increased tumor reactivity expression profiles. Notably, patients with HLA-matched TCR clones demonstrate improved overall survival. Our work indicates a complex relationship between genotype and TCR repertoire in the context of ICB treatment, with novel implications for understanding factors relating to therapeutic response and patient outcomes.

  Study EGAS00001008189

• Single-cell transcriptome analysis of B-cell development in the ABO platform

  The dataset includes samples from four individual donors, pooled at each cell-harvesting time point (days 21, 28, and 35). Single-cell RNA sequencing was performed on the 10x Genomics Chromium platform using GEM-X Single Cell 5′ v3 and GEM-X Single Cell V(D)J v3 for BCR profiling. For each timepoint, paired libraries were constructed: a 5′ GEX library and a V(D)J-B library. Per reaction 350,000-400,000 cells were loaded, aiming for 60,000 cells per reaction. Pooled libraries were sequenced on an Illumina NovaSeq X sequencer. 50,000 read pairs per cell for GEX and 5,000 read pairs per cell for V(D)J were targeted.

  Dataset EGAD50000002433

• RNA-seq dataset of Neoantigen Peptides derived from V(D)J-recombined Immunoglobulins Drive Outgrowth of Cytolytic CD8+ T-cells

  RNA-seq dataset of Neoantigen Peptides derived from V(D)J-recombined Immunoglobulins Drive Outgrowth of Cytolytic CD8+ T-cells

  Dataset EGAD00001015647

• V(D)J and 5' Gene Expression data on patients with aplastic anemia

  Chromium V(D)J and 5' Gene Expression platform (10X Genomics) was used to study patients with aplastic anemia. CD45+ cells from two patients (patient AA-3: 3 longitudinal samples from bone marrow and patient AA-4: 3 longitudinal samples from peripheral blood) were analysed. The raw data was processed using Cell Ranger 3.0.1 pipelines.

  Dataset EGAD00001006937

• Bulk-tissue RNA-sequencing paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex & cerebellar cortex – 4 individuals, putamen- 3 individuals)

  Profiling of paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen samples by bulk-tissue RNA-sequencing. Samples were derived from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex – 4 individuals, cerebellar cortex – 4 individuals, putamen- 3 individuals). Paired-end FASTQ files for each of the human samples are provided. Fastp (v 0.20.0), a fast all-in-one FASTQ pre-processor, was used for adapter trimming, read filtering and base correction. Fastp default settings were used for quality filtering and base correction. Further details on parameters used are available here: https://github.com/RHReynolds/RNAseqProcessing .

  Dataset EGAD00001009264

• HYDROXYMETH

  CpG hydroxymethylation. Software: minimap2 v.2.16; Megalodon.

  Dataset EGAD00010002418

• scRNA and V(D)J sequencing of WM under ibrutinib

  Single-cell RNA sequencing (5′ gene expression) and single-cell V(D)J sequencing (B-cell receptor and T-cell receptor) were performed on bone marrow mononuclear cells from patients with Waldenström macroglobulinemia treated with ibrutinib monotherapy. Sequential bone marrow aspirate samples were collected at baseline and after treatment. A total of 222 BAM files are included in this dataset.

  Dataset EGAD50000002279

• 10x Genomics BCR Sequencing

  BCR sequencing done with 10x Genomics V(D)J kit + platform for the paper: Integrated single cell analysis reveals co-evolution of malignant B cells and tumor micro-environment in transformed follicular lymphoma. Dataset contains paired FASTQ files for 35 samples, each was processed with the 10x Genomics V(D)J kit to obtain the sequence of the B-cell receptor sequence.

  Dataset EGAD50000001373

• IgM VDJ repertoire sequencing of 3 healthy donors using 8 different PCR conditions

  Peripheral blood mononuclear cells (PBMCs) were sampled from 3 healthy donors to sequence IgM heavy chain V(D)J repertoire libraries. Libraries were generated by targeting IgM heavy chain V(D)Js with a 5’MTPX primerset and sequenced on an Illumina MiSeq machine. Each donor was sequenced 8 times, varying only PCR amplification conditions, for a total of 24 sequencing libraries and therefore 48 paired-end fastq files.

  Dataset EGAD50000001510

• scRNAseq of patients with chronic graft-versus-host-disease

  This dataset contains 10 samples from 9 patients with chronic graft-versus-host disease (GVHD). Each sample is analysed with Chromium V(D)J and 5' Gene Expression Platform v1.1 (10X Genomics). The raw data includes fastq files for Gene expression and fastq files for V(D)J Expression. The processed data have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-13419.

  Dataset EGAD00001012121

• MiRNome_pituitary_adenoma

  Small RNA (<100 bases in length) were purified from total RNA using miRNeasy kit (Qiagen), then sequenced. Libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq small RNA protocol (Illumina), starting from 1 µg of high quality total RNA. Single read (1 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on miRBase v.2052, then counted with STAR (v.2.5.2a).

  Dataset EGAD00001004998

• Genome-wide association data on male-pattern baldness

  The study comprises 1000Genomes imputed data for 581 MPB cases and 416 male controls. Cases are selected for age<40 and Hamilton-Norwood grade V-VII. Control include 270 males >60 years no signs of AGA (Hamilton-Norwood grade I).

  Study EGAS00001001354

• Khoe-San Genome Project

  The dataset contains BAM files of whole genome sequencing data of African Khoe-San population (n=169, 30X coverage). DNA extracted from blood underwent 2 × 150 bp sequencing on the Illumina HiSeq X instrument (Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research). Raw sequencing reads were aligned against human reference hg38 including alternative contigs using bwa (v.0.7.15). The Genome Analysis Toolkit (GATK, v.3.5-0) was used for duplicate marking, indel realignment and base quality recalibration.

  Dataset EGAD50000002043

• Genetic Epidemiology of Ovarian Cancer Histotypes

  Epithelial ovarian cancer is a highly fatal malignancy with known genetic etiology; however, it is estimated that a substantial portion of narrow sense heritability remains to be discovered. The goal of this research was to use genetic information from distantly related ovarian cancer cases to identify regions of the genome that may harbor rare risk variants for epithelial ovarian cancer. The study was conducted in the setting of the Utah Population Database, a statewide data resource in which extensive ancestry data are linked to Utah Cancer Registry records. Focusing on families with a statistically significant excess risk of epithelial ovarian cancer, we used the Infinium Global Screening Array v.3.0 to generate germline genotyping data for distantly related cases. We then applied Shared Genomic Segment Analysis to each set of related cases to identify genomic regions that may harbor ovarian cancer risk variants. Eleven regions were identified. Genotype data are available through dbGaP for one case from each pedigree. Genotype data from other ovarian cancer cases within the high-risk pedigrees as well as the pedigrees' corresponding structures can be requested and made available with approval from the Utah Resource for Genetic and Epidemiologic Research (RGE).

  Study phs003140

• Neoantigen Peptides derived from V(D)J-recombined Immunoglobulins Drive Outgrowth of Cytolytic CD8+ T-cells

  Study EGAS00001008229

• RNA-sequencing of 82 pleural mesothelioma samples

  The dataset contains RNA-sequencing data (bam files) for 82 pleural mesothelioma samples. All the samples were sequenced on an Illumina NovaSeq 600 sequencer in paired-end mode, generating 100 nt length reads, to obtain an average of 60 million clusters for RNA. Demultiplexing was performed using Illumina bcl2fastq2. Fastq quality was assessed using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and low-quality reads were discarded. Sequence reads were aligned to Human reference genome (UCSC genome assembly GRCh38/hg38) using STAR (v. 2.7.0b).

  Dataset EGAD50000002131

• V(D)J and 5' Gene Expression data of bone marrow cells from patients with aplastic anemia

  Viably frozen blood MNCs from 9 cGVHD patients were sorted with BD Influx Cell sorter, to enrich for CD45+ cells. Gene and V(D)J transcript profiles were studied with 10x Genomics Chromium Single Cell Immune Profiling platform. The Chromium Single Cell 5’RNAseq run and library preparation were done using the Chromium Next GEM Single Cell Immune Profiling version 1.1 chemistry. The raw data was processed using Cell Ranger v3.1 pipelines.

  Dataset EGAD00001012117

• Bulk-tissue paired-end RNA-sequencing of anterior cingulate cortex samples derived from Lewy body disease patients

  Profiling of 24 human anterior cingulate cortex samples by bulk-tissue RNA-sequencing. Samples were derived from 5 non-neurological control individuals and 19 individuals with Lewy body disease (Parkinson’s disease = 7 individuals; Parkinson’s disease with dementia = 6 individuals; dementia with Lewy bodies = 6 individuals). Paired-end FASTQ files for each of the human samples are provided and are denoted by the suffixes R1 (read 1) and R3 (read 2). Fastp (v 0.20.0), a fast all-in-one FASTQ pre-processor, was used for adapter trimming, read filtering and base correction. Fastp default settings were used for quality filtering and base correction. Further details on parameters used are available here: https://github.com/RHReynolds/RNAseqProcessing/blob/master/QC/prealignmentQC_fastp_PEadapters.R.

  Dataset EGAD00001007698

• EGAD00010000536

  21 unlinked autosomal microsatellite loci for 30 Central Asian populations

  Dataset EGAD00010000536

• EGAD00010000538

  28 unlinked autosomal microsatellite loci for 20 African and 4 philippine populations

  Dataset EGAD00010000538

• scRNAseq of ALS patients

  The data set contains information from 9 individuals (5 ALS + 4 controls) using single cell RNA sequencing in combination with TCR V(D)J sequencing to study the immune profile of the central nervous compartment (CSF). Sequencing was done using 10x Genomics platform (5’ scRNAseq & V(D)J Reagent Kits v1.1). 5P and TCR libraries were then pooled and for sequencing on the NovaSeq sequencer. Provided files are in .fastq.gz format and per individual four files are available (Read 1&2 and Lane 1&2).

  Dataset EGAD00001009623

• Prospective Investigation of Pulmonary Embolism Diagnosis (PIOPED-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: To determine the sensitivities and specificities of ventillation/perfusion (V/Q) lung scans for acute pulmonary embolism (PE).Participants: A total of 1487 participants were enrolled.Conclusions: Almost all participants with pulmonary embolism had abnormal scans of high, intermediate, or low probability, but so did most without pulmonary embolism. Only in a minority of participants did the clinical assessment combined with the V/Q scan interpretation improve the overall chance of reaching a correct diagnosis of acute PE. Although a high probability scan usually indicated the presence of PE, only a small number of participants with PE had a high probability scan. Reference: PIOPED Investigators, 1990, PMID: 2332918.

  Study phs004020